How do you change opacity of grease pencil strokes in blender 2.8?
Okay I guess I am going to answer my own question. Because grease pencil is its own object now the color palette is no longer there, each grease pencil object will have its own material. If you want to lower the opacity you have to go Materials and under stroke click on color and lower the alpha channel. As for making new layers, you can just make new keyframes. 

Edited: I was mistaken there is another way to decrease the opacity, if you click on the grease pencil icon on the left side of the material tab you can also see the old layer opacity.